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alignment

DNAseq alignment pipelines for use on HPC systems.

alignment2

Will evolve to the new alignment pipeline to be run on cloud instead of cluster

beta-somatic-pipe

A dev version of somatic calling pipe used by cbttc for wgs and pnoc

bioconductor.org

Website for bioconductor.org

clustermap_tools

Somewhat specialized python scripts to create unsupervised hierarchical clustering heat maps

crispr_donor_pipe

echtvar

using all the bits for echt rapid variant annotation and filtering

filter_read_by_var

hgac_lims

django site to serve seqConfig

igsb_oxog_tools

ipython_notebooks

Collection of notebooks, mostly useful only to me

kf-sentieon-workflows

Sentieon workflow for Kids-First

kfdrc-toolbox

mouse_filter

Filter mouse reads from a Human PDX derived .bam

ngs_checkmate_wf

A cwl workflow to run ngs_checkmate on large datasets

openpbta-manuscript

The manuscript repository for the Open Pediatric Brain Tumor Atlas Project

openpedcan-analysis

The analysis repository for the Open Pediatric Cancer Project

project-specific

Repo with project-specific scripts. Not likely useful to general public

rnaseq

RNAseq pipeline

salmon-rnaseq

scRNA-seq pipeline using Salmon for quantification

seqconfig

Sequencing configuration generator

snf_robustinator

swift_seq_utils

variant_viewer_update_tools

Plugin to upload variant reports into variant viewer

variantviewer